Matrix: Rebirth
by wh1te rabb1t 01
Summary: Rebirth, restart, recycle. Everything that has a begining has an end. Sequal to Matrix: Virus.
1. Prologue: Rebirth

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Matrix: Rebirth

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_"Have you ever had a dream, Neo, that you were so sure was real? What if you were unable to wake from that dream? How would you know the difference between the dream world and the real world?"_****

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**Prologue: Rebirth**

The bullet flew through the chest, shattering bones, veins, and arteries. Blood seeped through the wound and onto the floor. Neo's vision began to fade. He saw Smith standing over him, watching. Everything went black.

Neo's heart beat slower. The flow of blood stopped. Death overtook him.

"Did it succeed?" the Agent asked.

"Yes. It is done."

"What do we do know?"

"Repair and recover. Destroy the Virus. Eliminate Zion. Send someone to gather the code."

"Yes, master."

"You did a good job, Matthews. But every good thing must end."

The Agent bowed low. "Of course."

The restart of the Matrix was more a shockwave of code restoration passing out from the Mainframe building. It caught Lynx in mid battle, shocking her. It passed Ghost as he lay in the dungeons of the Chateau. It passed the spot where the Oracle had been deleted, wiping out the last fragments of her codes. It flowed through Myst, yanking the Oracle's code from her, but leaving her with a vision.

_A figure stood with his back to Myst. He raised his arms and yelled. Destruction rained around him._

_ A train sped through a station. Morpheus lay on the floor, unconscious, while a large, unkempt man laughed hysterically. _

_ She saw a hovercraft fleeing a horde of Sentinels through the tunnels of the real world. Sentinels swarmed into Zion, spreading blood and fire in their wake. Shattered APUs littered the docks._

_ A massive ship, unlike any she had ever seen, floated beneath the ruined sky of the real world. It gave an almost bestial roar and launched bombs towards a glittering city on the horizon._

_ She saw a tall building. Smith stood on it, laughing. Seraph lay on the ground beside him, dead. She saw Trinity fighting the Twins. She saw Lynx running, Smith chasing her. She saw herself – burnt and bloodied – cradling Phoenix's head. Then she saw a single strand of code descending into blackness, and the Oracle's voice filled her thoughts._

_ "Change is the only constant in life. It is a dangerous game. Meet it well, Myst."_

The wave of rebirth swept the Oracle's code into the recycling bin of the system. Ever efficient, the bin's manager recycled the code, filtering it into two lesser programs.

These programs quickly took form. One was a woman with long, white hair and green eyes. She wore a swirling white cloak and black sunglasses. The other was a man, with black hair and pitch black eyes, who wore a black suit, black undershirt, black dress pants, and a dark pair of sunglasses.

The wave of code renewal passed through the clones of Smiths, destroying the, and returning the bodies to the control of their original inhabitants. The one surviving Smith stood over Neo, laughing still.

The wave also swept up Neo's code. It gathered the fragments spread over the Matrix by his death and bonded them into one program. This program suddenly found himself standing in front of a large pair of doors. He pushed them open.

The two programs created from the Oracle's code greeted him.

"Welcome to the lands of the dead, Neo."


	2. Causality

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Part One: Motions and Metaphors

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_ "I do not see coincidence, I see providence, I see purpose. I believe it is our fate to be here. It is our destiny. I believe this night holds for each and every one of us the very meaning of our lives."_****

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**Chapter One: Causality**

Myst was on her hands and knees, panting. Seraph knelt down beside her.

"You have seen a vision. The Oracle gave up her code for it to happen. You must be worthy of her last gift."

"The Oracle gave up her code? What does that mean?"

"It means she was deleted."

"No!"

"She knew it would happen. She also knew her code would be recycled into two lesser programs that are needed to help Neo return to the real world."

Morpheus rubbed his eyes and stared in shock at Neo's dead body.

"He's gone…It can't be. He is the One!"

From behind Morpheus, Phoenix watched the code spiral down the screen. He hit the button, bringing up the view of Trinity strapped to a chair inside the Matrix.

"Morpheus, I know you're in shock, but you have to send me back in."

"Alright."

"Damn it, sir, I have to get back…did you say alright?"

Morpheus nodded.

"Thank you, sir. I'll bring them back…I'll bring them all back. Load me up."

"Already started."

"No," Myst said. "We need her."

"There is very little left she could have done," Seraph explained. "Her purpose has been fulfilled. She set into motion the events that may break the cycle. Neo is the most powerful rebel there has ever been, and he has the ability to stop it all. But he will need help."

"So Neo is alive?"

"No."

"What happened?"

"I do not know."

The man who had been Neo in a former life looked around the entrance to the Chateau before.

"I've been here before…" he said.

"Actually," the woman said, "you haven't."

"I remember it so clearly."

"Patience. All will be told in due time."

"Who are you?" the man who had been Neo asked. "I know you."

"You do know us," the second man said. "In a former life we were part of the Oracle, but now she is dead. I am Samsara. My female companion here is Mukti."

"Who am I?" asked the man who had been Neo.

"You were once a human," Mukti said. "A human of great power. But Smith tracked you down and killed you when you were most vulnerable. You died, but as the Matrix restarted it accidentally recycled your code and made a program of you."

Samsara took up the tale. "When you were killed, you touched the Source. You took on the aspects of every One before you. You have their memories and their personalities inside you, Neo."

The man shook his head, as if trying to clear it. The mention of his name seemed to brighten his face a little.

"Forgive me," he said. "I am…a little confused."

"That is understandable," Mukti said. "But the two of us have found a way to get around the memory wipe you were given."

"What way would that be?" the man asked.

"It is just a name: Trinity."

- _lips pressed against lips, a hand against flesh, the sweet smell –_

Neo gasped. "I remember her," he said, smiling.

"I thought you might," Samsara said, also smiling. "Welcome to the world of the dead, Neo."

Lynx looked around in shock. The Smith copies had vanished.

"What the hell is happening?" she said to herself. On the horizon she saw a bright flash of green coding as the sun rose on a new day.

"This place gets weirder every time I come in," she lamented. "I need to find an exit."

Her phone rang.

"Captain?"

"Yes. Trinity has been captured by Agents. I've sent Phoenix in to help, and I am about to call Myst. The three of you will meet at the Adams Street bridge. Then you must save her."

"Sir, what happened?"

"As far as I can tell, the Matrix has been restarted. Smith is gone, clear off the map. Neo is nowhere to be found as well. Ghost has been taken by the Merovingian."

"Shit."

"We need to get Trinity out so she can help you rescue Ghost."

"Yes, sir."

"You said that before. What, exactly, does it mean?" Neo asked.

"You are now dead," Mukti explained. "You have lost contact with everyone you once knew and cherished. They believe you dead, as do the machines. Only we Exiles know the truth, that you have been reborn as a program."

"So I am alive?"

"In the technical sense of the word, no. Your body has stopped functioning. Even now, as the false sky begins to poor an unending rain, Morpheus lays you under the funeral shroud while a tear falls from his eye."

"And in the mental sense of the word?"

"Yes. Your mind lives on inside the Matrix."

"Can I ever see the outside again?"

"Why?"

"What?"

"Why? Why would you want to? Why not stay here, with us, and study? Is it not better then a life of unending war and conflict?"

Neo thought for a long moment.

"I have duty," he explained. "Duty to those still alive. I must fulfill that duty." 

Samsara smiled. "Exactly."

"Why are you two leading me along?" Neo asked in a sudden burst of rage. 

"We are here because it is our purpose," Mukti said. "We are here to train you so that when your friends come for you, you will be ready."

"My friends? They will find me?"

"Maybe. If they do, you must be ready."

Phoenix stood under the bridge in the relative dryness, looking outward. At the far end of the street, Lynx appeared, walking towards him. She raised a hand in a tired greeting. He smiled slightly. 

Myst and Seraph appeared under the bridge.

"Phoenix!" Myst said, flinging her arms around him. He looked surprise and then wrapped his arms around her, pulling her closer. Lynx coughed discreetly.

"Right," said Phoenix, breaking apart from Myst. "We still have a job to do."

"And where exactly am I here?" Neo asked, waving his hand around him.

"Haven't you guessed yet?" Samsara said incredulously. "We're in the Chateau."

"I have never been here," Neo said.

"You haven't," Mukti said, "but _she _has. Look inside yourself. Find the softest voice within."

_The Merovingian laughs. Laughter is a luxury I cannot afford. I roll sideways and fire my weapon at him twice. He lifts a hand and stops the bullets._

_ Impossible! He yanks out a gun and points it at me, firing. Pain in my side. Hard to breath. Blood pouring out of my wound. It's all going black._

_ No! Must…not…fail…lifting my head now. He sees me. I see him. He _fears _me! I see his fear. Power flowing through me, enveloping him in fire. we both burn. I pass from this world._

_ They are safe._

Neo blinked his eyes. "What was that?"

"That was the voice of your memory," Samsara said. "Specifically, the voice of a young woman known as Dagger. She was an anomaly three emersions before you. She died in the Chateau before ever reaching the Source, died to save her lover. It was a disaster. The whole system almost crashed. One Agent, however, managed to save it."

"Smith," Neo said with utter conviction.

"Exactly," Mukti said. "But he gathered to himself a failsafe against deletion in that time, so if an anomaly ever defeated him he would survive to get revenge. And now that is his only goal."

"There is a weak point in the Mainframe building here," Phoenix explained, pointing to a spot on the blueprint.

"One bomb there could bring this whole section of the building down," he explained. "Myst, that will be your part.

"After the section goes down," he continued, "Lynx and I will go to find Trinity. She's somewhere on the thirteenth floor. Seraph and Myst will distract the Agents."

They both nodded. Seraph stood in the corner, silent. Phoenix looked around.

"Let's go."

Myst nodded to Seraph as they approached the metal detectors. She reached inside her bag and pulled the pin on the grenade inside, sliding the bag into the x-ray machine. The she grabbed Seraph and ran backwards.

A guard looked up when the x-ray buzzed.

"Oh, shit," he said as the grenade exploded. Myst opened fire, cutting down the other two guards.

"That was easy," she said. "Let's go."

She led Seraph down a long hallway, the programming following behind with both guns drawn. Myst looked cautiously down another path and stepped out into the open.

"This is _almost _too easy," she whispered to herself. From down the hallway, two Agents stepped out of a door.

"Shit," said Myst, turning around. "We'll have to find another way."

Seraph shook his head and stepped forward. The Agents looked at him.

"Destroy him," ordered the first. The second Agent stepped forward and swung a fist at Seraph. Seraph grabbed the fist and twisted it, hearing bones snap. He pulled the Agent in and leapt into the air, kicking the program in the head. He stumbled backwards and crashed into the other Agent. They both rose.

They rushed forward and attack at the same time. Seraph ducked under a fist and hit one in the stomach, sending him into a wall. He slammed a kick into the other one's side, knocking him to the ground. The Agents lay motionless.

"How are you so powerful?" Myst asked.

"Don't you believe in angels?" Seraph asked, continuing down the hallway.

"What _is _Smith?" Neo asked. "He can't just be an Agent."

"He never was _just _an Agent. He was the first Agent. The most powerful. But while they updated his software, they never updated his driver. He grew to hate the humans, and let those emotions rule his actions. It made him the most successful, and the Motherboard was afraid to cut back on his programming. He destroyed himself."

"What is he doing with his copies?"

"He seeks to control the Matrix. Once he controls everyone inside, he will bring it down and spread out into the real world like a fire. Nothing will be able to stand in his way."

"He must be stopped."

"Yes."

Myst slapped a bomb onto a support pillar and started running. Seraph slammed into a door, knocking it off its hinges and out of the way. The two fighters made it to the lobby as the countdown reached zero. A wave of fire spread through the hallway, shooting out of the doorway and filling the lobby. The building groaned and began to collapse.

Phoenix and Lynx watched the building fall from across the street. When the dust settled, a corner of the office building was missing. 

"It's time," he said. Lynx nodded and ran across the street. Phoenix followed her. She leapt up and grabbed the bottom rung, pulling herself up the fire escape and onto the second floor. Then she helped Phoenix up.

"Eleven more," she said, beginning up the stairs.

They reached the thirteenth floor. Lynx kicked open the door and pointed her two pistols inside.

"Clear. They must have fallen for it."

"Let's not waste time," Phoenix urged. The two ran down the hallway, reaching the room where Trinity was held. 

"One…two…three…" Lynx said, kicking open the door. Phoenix instantly targeted one Agent with each gun and started firing. They moved to dodge his bullets and he shifted his aim, firing at their bodies. Lynx turned her guns on them, and the combined firepower took them out.

Lynx rushed forward and pointed her gun at Trinity's handcuffs, squeezing the trigger. The cuffs came off and Trinity stood up, rubbing her wrists.

"Thanks," she said.

"Don't mention it," Phoenix said.

"Neo?"

Lynx shook her head. Trinity closed her eyes and leaned against the wall. The other two rebels waited in silence a few moments.

"Let's get out of here," the woman said. Lynx nodded in agreement.

"Morpheus, where's the nearest hard line?" Myst asked.

"Far," the captain answered. "You're inside the core network."

"Which way?"

"Left. You need to get three miles to the south."

"That will take a while," Myst said. She slowed down as a particular vehicle at the nearby hospital caught her eye.

"Do you see that, sir?"

"Yes. Can you drive it?"

"Not yet."

Supported between Phoenix and Lynx, Trinity limped out of the Mainframe building. They heard a sharp, cutting sound in the sky above them and looked up. A helicopter descended to land in front of them. Seraph waved them on. They gratefully piled into the craft as Myst took off again.

"Which way?" she shouted. She waited for an answer, and then turned the helicopter to the south. They flew in relative silence for a few minutes, and then the helicopter descended and set down next to a pay phone. They were finally out.


	3. Purgatory

**Chapter Two: Purgatory**

A phone ringing jolted Neo out of his silent reflection. He glanced over at Mukti, who pointed to a small touch-tone phone hanging on the wall.

"It's for you," she said. His confusion only grew. Samsara got up and walked to the phone, answering it. He listened and beckoned Neo over. Neo got up and walked to the phone, taking the receiver from Samsara.

"Hello?"

"Mister Anderson," said a familiar voice at the end of the line. "I thought you had survived. It seems as long as one of us lives, the other cannot die."

"So it does."

"The reason I have called, Mister Anderson, is to tell you that I your time draws short. Somehow you escaped my grasp, but you will be mine soon."

"This isn't over, Smith. Not by a long shot."

"Oh, yes it is. And you have lost. The rest of you hasn't realized it yet, but your mind knows, doesn't it? I am a machine, Mister Anderson, quite literally. I will hunt you down. I will never tire, and I will never stop."

The line went dead. Neo hung the phone back up, then suddenly snatched the receiver back.

"This line reaches the outside?" he asked. Mukti nodded.

"Good."

"Call incoming!" Myst shouted from the Core. Morpheus came over and grabbed the headset from her.

"This is Morpheus. Who is this?"

"Morpheus!"

"Neo?"

"Yes, sir."

"Impossible. He's dead. Who is this?"

"Captain, listen carefully. This is Neo. I don't fully understand what happened myself, but the restart of the Matrix apparently triggered a rewriting of me. I am in the Chateau right now, living as an Exile. I am here with two programs created by the Oracle's code."

Myst leaned in from behind Morpheus.

"Seraph mentioned two such programs to me."  
"Okay, is this is Neo, tell me something only he would know."

"Morpheus…"

"What?"

"Fine…Remember that time during my first visit to Zion? I tried to flush a toilet and wasn't sure which button to press…"

Morpheus started laughing.

"That one I do remember."

"Morpheus, I need help."

"We'll get you out."

"That's just the thing. I've been informed that the Chateau has been removed from the Matrix, that it's impossible to reach by normal means."

"What do we do?"

"Well, hold on. There's someone who can explain this better."

Morpheus and Myst heard the phone being passed from hand to hand, and a feminine voice emerged from over the line.

"Hello, Morpheus."

"Who is this?"

"My name is Mukti. I need to tell you how you can get here. There is a man inside the Matrix known as the Prophet. He was the companion to Samsara and I in our previous form. Lynx has met him. He can tell you what to do."

"Alright, but – "

"Our time is brief. I must go."

She hung up.

Neo glanced at Mukti.

"Why such a hurry?"

"Seraph is coming."

At that moment, the doors swung open and Seraph walked in.

"Greetings," Samara said. "We've been expecting you."

"Of course," said Seraph. "Neo."

"Seraph," Neo returned.

"I am glad to see you survived your ordeal," Seraph said, "though not in a physical sense."

"Yes, I'm glad too," Neo said.

"However, I must apologize."

"You are here to test me again?"

"Yes. I must measure your hearts resolve if you wish to pass these doors back into the world of the living."

Neo bowed to Seraph. The guardian bowed back and squared off into a fighting position. Neo swung his left foot in and Seraph jumped over. The program flipped to land behind Neo and struck him in the neck, sending him stumbling forwards.

Neo turned around and jumped up, kicking out with both feet. Seraph batted both blows away and moved in close, striking at Neo's chest. The man flipped over and landed on his feet far away. He motioned Seraph forward.

Seraph dashed forward, sliding at Neo's feet. Neo jumped over his attack and landed behind him, dashing at the program. Seraph leapt to his feet and blocked Neo's fist, hitting him in the stomach and sending him crashing into a wall. Seraph held up a hand.

"Enough."

Neo climbed to his feet. 

"I'm not done yet," he said. Seraph nodded and attacked. Neo blocked a slashing blow and jabbed Seraph in the chest with his fist. The program grabbed Neo's fist and twisted it. Neo flipped sideways with the counter and landed on his feet, yanking his hand from Seraph's. The program jumped and kicked at Neo's head. Neo jerked his head back and brought his hands up, propelling Seraph over him. Seraph twisted in midair and landed on his feet. He hopped onto one foot and kicked Neo in the chest. Neo flew through the air and fell to the ground, stunned.

"I'm sorry," Seraph said, "but you are not ready yet."

He walked from the room.

Samsara helped Neo to his feet.

"And that is why we are here, Neo. To help you."

Neo floated in the center of the room, legs crossed and arms folded. His eyes were open, and his sunglasses lay on the ground. 

"Center yourself," Mukti said, her voice cutting through the silence.

"I am," said Neo, breathing out. Samsara nodded in satisfaction. 

"Fight me," he ordered. Neo dropped to his feet. Samsara started forward, striking at Neo's head. The One blocked his attack with a fist and moved backwards with it, dragging Samsara across his foot and tripping him to the ground. Mukti leapt in, hitting Neo in the chest with a roundhouse kick. Neo flipped in midair and landed on his feet.

"Patience," Samsara coached. "Release will come."

Mukti came in from the side, swinging a fist. Neo blocked with his left and hit her with an uppercut from his right. She stumbled backwards and Samsara darted in with a straight kick. Neo batted the leg aside and ducked past the program's guard, striking him once and sending him flying. Mukti grabbed Neo and pulled him backwards. He stumbled backwards, and Mukti hopped into the air and hit him in the chest with a quick kick. Neo flipped over backwards to land behind Samsara. 

Mukti held up her hand.

"We have visitors."

The Merovingian and Persephone had both entered the room, flanked by the Twins. The four came to a stop before Neo.

"This was not wholly unanticipated," the Merovingian said. "And now that I have you, the question is _what _shall I do?"  
Neo was calm. "Merovingian, the only solution that leaves you alive is to let me go. I do not make idle threats, I am only warning you. Release me."

"Release you?" the Merovingian laughed. "You are dead, boy. I thought these two" – he indicated Samsara and Mukti – "would have made you realize that by now. I cannot do anything to harm you. You however, cannot leave this room, or do anything to harm me, until you have passed the guardian. And you will never pass him. He is too strong, and you are too _ weak._"

The Merovingian left. Persephone stayed behind.

"What do you want?" Neo asked tonelessly. "A kiss in exchange for freedom?"

"My _husband _and I seldom agree," she said. "But on one thing we do. We need you alive, and here. He wants you as leverage over me. I need you to destroy Smith."

"What?"

"Haven't you guessed yet, Neo? The Mother of the Matrix – the Motherboard? She and I are one."

"I know him," Lynx said. "He met me at the Oracle's once and guided Neo to the Source."

"Where can we find him?" Morpheus asked.

"I don't know."

"Think, Lynx," Trinity urged. "Neo's life could depend on it."

"I remember him from the Oracle's apartment," Lynx said, shrugging. "That would be a good place to start."

"Let's go," said Trinity.

Neo had another companion in the world of the dead. Ghost was there, unharmed but unresponsive. He lay in a coma on the ground, eyes open and staring into nothingness.

"The Merovingian has trapped him in his own private hell," Mukti said.

Neo nodded. "Can I help him?"

"There is a way, but it is dangerous," Samsara answered.

"What?"

"If you enter his dream world and defeat his foe, you can free him. He will wake aboard your ship."

"Send me in."

Neo opened his eyes to the City. Ghost stood in the middle of the clearing, doing battle with the man Neo knew as Drake.

"Neo!" Ghost shouted. Drake turned.

"They will pay for this," he said. He turned to face Neo. Neo broke into a run, dashing at Drake. Drake swung at his head, but Neo blocked the blow and returned it with more force. Drake jerked his head to the side and pushed up on the attack, sending Neo's arm out of the way. He turned his move into a jump and reverse kick. Neo's head moved with the attack, and his body came around. A fist struck Drake in the cheek and sent him flying.

Drake climbed to his feet, wiping dirt from his cheek. 

"You'll pay for that," he spat, along with a glob of blood. He dashed forward again. Neo sidestepped and tripped him, sending him flailing. Drake climbed back to his feet and rushed at Neo. Neo blocked a high attack and jammed his fist into Drake. Drake stumbled backwards two steps.

Neo smiled grimly. Drake hissed in agitation.

"You haven't won yet, boy."

Neo jammed his hand into Drake as he had seen Smith do. Neo concentrated, and a program spread out from his attack. Drake screamed as the deletion overtook him. He vanished in a flash of code.

Ghost opened his eyes aboard the _ Nebuchadnezzar. _Myst was at his side in an instant.

"Ghost?"

"I'm fine."

"What the hell happened?"

"Neo got me out somehow."

Myst marveled. "Even when he's dead he helps us."

"What?"

"I have a lot to explain."

Lynx opened the door to the Oracle's apartment.

"Trinity, over here." 

The woman came over and looked at what Lynx was holding. It was an old, slightly bent spoon.

"What do we do with it?" Trinity asked. As the two watched, the spoon slowly melted away in their hands. A door opened in the hallway.

"Greetings Lynx," the Prophet said.


	4. Breaking the Cycle

**Chapter Three: Breaking the Cycle**

Behind the glasses, a rebel was safe. No one could see through the dark shades, through the windows of the eyes, and into her soul. But the glasses were gone now.

Morpheus stood, quietly, reverently, in front of the assembled group. Trinity stood facing him, and behind the two of them stood Phoenix, Myst, and Lynx. They had bowed their heads in respect.

"Life is a journey," Morpheus said. "I have always envisioned it as the sailing of a great ship, back in the days when the sky was still blue and the surface was green. The ship spends a long time on land, being slowly and carefully built, every aspect of it being lovingly planned by people totally dedicated to its construction. Then, one day, the ship is finally ready. It is launched from the docks where it has spent its entire life and allowed to go its own way.

"As the ship travels, it begins to grow smaller. First, the hull disappears beyond the horizon. It seems as if the ship is being sucked into the water, but it is not. Eventually, the optical illusion swallows the sails and the ship disappears. People mourn this vanishing. But the ship continues its journey, and it comes into view of its destination, where other voices pick up a call of welcoming."

Lynx was crying now, one tear slowly making its way down her face. The tear made its way to the bottom of her chin and fell, traveling through the air until it struck the ground below. The fragile drop shattered, splattering the surrounding area with water. More drops hit the ground around the tear as it began to rain.

"Rabbit, Pandora, Voyd, Angel," Morpheus continued. "These are but a few of the names we have had to add to our list of the dead recently. But we cannot forget _why _they died: so that we could go on living. Let us not be unworthy of their sacrifice."

The rebels stood for a minute in silence. Then Trinity's voice rose into their minds.

"Now let's go get Neo so we don't have to add another."

As one, the rebels replaced their glasses on their faces. The Prophet smiled. Morpheus led their way.

Neo awoke back inside of the Chateau.

"What happened?" he asked. 

"Ghost was saved," Mukti said. "He woke aboard your ship. Now you must past one last test before facing the Guardian again."

"What test is that?" Neo asked.

"You passed through the trial of Fire, when you saved your captain from sure death. You passed through the trial of Blood when you experienced death yourself. You rescued Ghost to complete the trial of Release. Only three trials remain before you are ready to face your destiny."

"What trials are those?"

"The trial of Rebirth," Samsara said.

"The trial of Balance," Mukti added.

"And the trial of Fate," said Samsara. "This is the trial you face now."

And the world fell away beneath him.

"Where is Neo?" Trinity asked, looking at the Prophet.

"He is trapped in a place between this world and ours," the Prophet said. "When he was killed, the Motherboard tried to eliminate him, but the Merovingian was too quick for her. He swept up Neo's code and deposited it into a safe place, a storage facility. He locked the door with a powerful program named Seraph."

Trinity and Lynx glanced at each other.

"But," the Prophet continued, "Unbeknownst to the Merovingian, the Motherboard has an avatar inside his organization. She is just biding her time and waiting to strike."

"Then we'd better hurry," said Trinity.

"Indeed," said the Prophet.

Morpheus stood and watched the two women go. One, his faithful second mate since before Neo was unplugged, the other, a brave young fighter. He smiled. They'd do fine.

He turned to Myst and Phoenix.

"Let's go," he said. He pulled out his cell phone.

"Ghost, I need an exit." The former _Logos _ crewman had an Operator training download, and was now serving as the _ Nebuchadnezzar's _Operator as he recovered from injuries.

"Got one coming up, sir," Ghost said. A nearby pay phone rung. Morpheus lifted it to his ear and vanished. Phoenix lifted it up and replaced it on its hook. Then he heard a gasp from behind him and turned around.

Neo stood in the middle of the street as rain pounded on the ground all around him. He looked up and saw Trinity begin to fall. He began to take a step forward.

Mukti appeared in front of him.

"Trinity falls," she said. "To certain death. But you _can _save her. There is a small window of opportunity. You can save her, be freed yourself, and return to Zion…only to see it fall. Or, you can let her die, remain here, and Zion will be saved."

"No," said Neo. "Not possible."  
"Why not?" she asked.

"How would something you described happen?"

"False dependencies and distractions, Neo. But the moment has come. Save her and kill your species…or save them and watch her die. Choose, and act."

Samsara spoke up. "It is a choice you would have been forced to make under other circumstances. And now you must make it anyway."

Neo's foot wavered in the air, halfway between where he stood and where he walked towards. His foot suddenly came crashing down, creating a splash in the water. He pushed off the foot and dove, flying towards Trinity. As her body hit his arms, the world faded away.

"Why?" asked Mukti's voice out of the blackness.

Neo smiled, a gesture no one saw. 

"This is the trial of fate, right?" Neo asked. "Well, fate is bullshit. Nobody controls my life."

The Chateau reappeared in a flash of light and coding. Mukti stood before him again, smiling. 

"You passed, Neo. Now you must pass the trial of Rebirth."

Seraph entered the room.

"There is a program called the Trainman," the Prophet said. "He runs the trains that run throughout the Matrix. IF you can find him, you can force him to lead you to the Chateau, where Neo is held."

"Sounds easy enough," Lynx said.

"I've never put faith in that," Trinity said.

"Of course not."

"The Trainman will be coming through the nearby station in about ten minutes. We need to move."

Phoenix remembered him, the man called Lucifer. He stood there, glaring, his eyes twin points of fire. It seemed he remembered Phoenix as well.

"We meet again," Lucifer said. "This time, however, I shall prevail."

He came forward. Myst darted in and took a swing at him, and he hit her, palm open, in the chest, sending her flying away. He advanced towards Phoenix. Phoenix dashed left, drawing his pistol and firing twice. Lucifer drew his own pistol and fired once.

The bullet flew forward and struck Phoenix in the hand. Phoenix swore and dropped his gun. Gunshots sounded again, and Myst's attacks sailed past the Exile.

Lucifer twirled his gun over his shoulder and fired twice. Myst bent backwards, and the first bullet sailed over her. The second one struck her in the leg, and she cried out and fell to the ground.

Phoenix came forward and kicked upwards, hitting Lucifer's gun out of his hand. He dropped the first foot and brought the second one up, hitting Lucifer in the chest as his first foot touched the floor. The Exile flew into the air, twisting around and landing on his feet. He dashed forward again.

"What's happening?" Morpheus asked.

"An Exile," Ghost said, pointing to a stream of coding. 

"Shit."

"Are you going to help them?"

"I can't. Every time we jack in it increases the chance that a Sentinel will find us. We don't want that."

"True enough."  
"And they can handle one Exile, I'm sure."

Neo bowed to Seraph for one last time. Seraph started in first, swinging his arm out towards Neo's head. Neo bent back to avoid the blow and came around and under, hitting Seraph upward in the stomach. The program rose off his feet and stumbled backwards. 

Neo followed up with a roundhouse kick from the left, which Seraph blocked with one hand. The program grabbed Neo's foot, and Neo twisted in the air, bring his other foot into Seraph's face. The program let go of Neo and sagged sideways. Neo brought his feet back under him and landed in a fighting stance, waving Seraph forward. Seraph nodded and advanced.

"Here," the Prophet said. "This is the station."

"What do we do now?" Lynx asked.

"We wait."

Phoenix blocked a sideways swing and slammed his fist into Lucifer's head, rocking it backwards. The Exile kicked out, hitting Phoenix's knee, and the rebel grimaced in pain, staggering a step backwards. Lucifer grinned and slammed his fist into the right side of Phoenix's head. Phoenix moved with the blow, using his momentum to turn and bring his right foot into Lucifer's side.

Lucifer groaned and grabbed the foot, slashing it with his claws and shoving Phoenix forward. He slammed into the ground hard and tumbled to a stop a few feet away. Phoenix's hand grabbed for his gun, and he found it on the floor and fired at Lucifer.

Lucifer jumped into the air, spreading his wings. Phoenix fired twice, shredding Lucifer's left wing. The program came falling out of the sky, crashing into the ground. He lay still.

Neo jumped into the air and kicked off the wall. Seraph copied the move from across the room. They flew towards each other and met in midair, Neo hitting Seraph with a vicious uppercut that sent him flying towards the roof. The program crashed through the ceiling, and Neo flew up after him.

Neo landed on the roof as rain poured down around him. Seraph picked himself up and leapt at Neo, swinging a foot to meet Neo's fist. Neo was lifted into the air and spun sideways, and he landed at the edge of the roof, holding on by his hands. He swung up and hit Seraph, in the chest with both feet, sending the program toppling across the edge of the roof.

Neo landed on his feet and advanced towards Seraph, who lay on his back. Seraph brought his legs together around Neo's feet and twisted his body, rising to his feet as he brought Neo down. He brought a fist down to meet Neo's head, but the rebel had already rolled away, and the fist left a crater in the roof. Neo rose into the air beside Seraph and kicked him in the side. Seraph fell off the roof and towards the ground below.

Phoenix pointed his gun down at Lucifer's form. He pulled the trigger three times, and saw the bullets enter the program's head. Phoenix then sank down onto one knee, cradling his injured leg. Myst rose from the ground and limped towards him, a bullet wound near the edge of her thigh.

"He's not dead," Phoenix said. "But that should stall him."

Myst nodded wearily and they made their way towards the hard line. Myst lifted the phone first, closing her eyes as she felt herself yanked from the Matrix. Phoenix replaced the phone and waited for it to ring.

"No…" came a voice. Phoenix turned as he reached for the phone. There was a gunshot, and as Phoenix placed the phone to his ear, he felt a bullet enter his stomach.

Seraph stopped his wild fall and ascended back towards Neo. Neo flew towards the program, flinging a fist into Seraph's face. Seraph took the blow and flew backwards a few feet, stopping himself and launching a counter-attack. Neo blocked a kick and grabbed Seraph's leg with both hands, throwing him back through the roof and into the room far below them. Neo dove downwards.

"Shit!" said Ghost as the alarm beeped on Phoenix's chair. Phoenix opened his eyes the moment the gunshot wound appeared in his stomach, spurting blood. 

"Get the med kit," Morpheus ordered, rushing towards Phoenix. "Myst, get me one of Neo's spare shirts, hurry!"

Myst ran off. Ghost returned with the med kit, dropping it onto the table beside the operating chair. He extracted a syringe and plunged it into a plug on Phoenix's arm, injecting a painkiller into his system.

Myst returned with the shirt, and Morpheus pressed it to the wound, trying to stop the blood flow. Phoenix gasped as Morpheus pressed down on the wound, his grip on the side of his chair tightening. He gritted his teeth.

"This…isn't…real…" he said to himself. Morpheus grabbed a roll of tape from the med kit and wrapped it around Phoenix's wound, holding the makeshift bandage in place. 

"Get the plug out, Myst," Morpheus ordered.

"This…isn't…fucking…real…" Phoenix said, almost shouting. The blood suddenly stopped flowing. Phoenix gave a gasp and relaxed backwards.

"Phoenix?" said Myst, frozen, holding the plug halfway in and halfway out of Phoenix's head. Morpheus ripped open Pheonix's shirt.

"The wound's…gone…" he said. Ghost glanced at the medical readout attached to the feed.

"Shit," he said again. "Morpheus!"

Seraph jumped to his feet as Neo glided to a smooth landing inside the room. The program dashed forward, sliding at the last moment and hitting Neo in the foot. Neo fell forwards, grabbing Seraph and pulling him down.

Neo kicked out and sent Seraph flying into a wall. He climbed back to his feet as Seraph regained his.

"No more," Seraph said. "You are wearing down, Neo. You're not a superhuman anymore. More of this will kill you."

"I can't stop," said Neo, walking forwards, slowly, tiredly.

"And why not?" asked Mukti, suddenly.

"I can't let them down," Neo said. "Everyone depending on me. I can't fail them. I must keep going…Even if it means my death."

Mukti nodded and stepped forward, catching Neo and holding him. She kissed him on the lips. Power flowed through her kiss, rushing into Neo and reenergizing him. He looked back at Seraph.

"You can't do that," Samsara said, clearly shocked.

"I just did," said Mukti, smiling. "I am the release; you should have seen this coming."

Samara nodded. "True."

Neo faced Seraph again. 

"Let's go. This is the last time."

Seraph nodded and rushed forward. Neo punched straight out, hitting Seraph in the chest. Seraph flew backwards and hit the wall, leaving a crater. He crashed to the ground and lay still.

"What now?" Neo said.

"You are free."

Morpheus glanced at the part of the readout Ghost indicated.

"An aneurism?" he asked. "How?"

"I don't know," Ghost said. "It may have something to do with the disappearing gunshot wound. But he's gone."

Even as they watched, Phoenix's heart rate slowed. It suddenly reached zero, the beeping filling the cabin at a constant rate. The next sound was the plug hitting the floor as it slipped from Myst's suddenly limp hand.


	5. Interdependance

**Chapter Four: Interdependence**

The rain continued to pound the ground in the Matrix.

"Something is seriously wrong in their," said Ghost. "Look."

He touched part of the screen, zooming in on a section of the code.

"This rain is unlike anything I've ever seen," Ghost said. "It's not the normal coding."

"What could it be?" Morpheus wondered.

"I don't know, but it can't be good."

Neo stood at the exit to his prison.

"Goodbye," said Samsara. "And good luck."

Neo took a step outside. The Chateau fell away beneath him. His foot hit the ground again inside a puddle of rain. He glanced ahead and saw Smith waiting for him.

"Mister Anderson…Welcome back. We've missed you."

The Merovingian burst into the room where Samsara and Mukti still were.

"You let him go?" he asked incredulously, almost spitting with rage.

Samsara nodded. "He is gone now."

The Merovingian threw up his hands. "This cannot happen. You two – " he indicated the Twins " – go get him back."

The two albinos nodded and turned simultaneously; walking through the door Neo had stepped through.

"Now," the Prophet said. Lynx faintly heard a train approaching the station. She stepped out to wait on the platform, coming up beside Trinity.

The train slowly pulled into the station, coming to a stop. The doors slid open and three passengers got off, a man, a woman, and a young girl. The girl looked at Trinity and opened her mouth to speak, but her father pulled her out of sight.

The Trainman came to the door and looked out, his eyes catching sight of Lynx.

"What do you two want?"

Trinity started forward, grabbing the butt of her gun. "We need to take your train."

"No deal," said the Trainman.

"We're getting on the train," Trinity said. "Wither you like it or not."

Lynx saw the Trainman start to move and drew her gun as he went for his. His gun came up and pointed at Trinity. Lynx's gun was aimed at his head. Trinity was frozen, her hand halfway to her own sidearm. 

"Don't move," the Trainman warned.

They heard footsteps approaching from the entrance to the train station. Lynx turned to see an Agent enter, holding a gun. As Lynx brought her second gun out to bear on the new threat, the Trainman slapped the "door closed" button. The train began to move away.

Morpheus looked over Ghost's shoulder at the Matrix code spiraling down the screens.

"Agent Matthews," Morpheus said. "Jack me in."

Ghost nodded and began typing.

"I must admit, I am somewhat relieved to see that the Merovingian did not get to kill you himself. I reserve that pleasure for me, and me alone. Of course, I've already killed you once…just as you have killed me once. Then I killed you again…and I myself died by plans you set in motion. So we continue in this cycle of death and destruction until I kill you again…and this time, you will not come back."

Neo did not respond, glaring across the gulf that separated him from Smith.

"Well then, let us begin."

Neo's hands curled into fists as the rain continued to pound around them. He exploded into motion, running at Smith. The program rushed to meet him, and they clashed at the midway point.

Neo swung his fist straight out, and Smith bent backwards. Neo let his momentum carry him into a flying kick, knocking Smith back a few steps. The program rushed back in, hitting Neo twice in the stomach, lightly, before his blows were pushed away. Neo returned the attacks, hitting Smith in the neck with an open-handed blow.

Smith dragged his left foot up and hit Neo's side hard. The rebel grabbed Smith's foot and tossed the program to the ground a few feet away. Smith slowly rose to his feet, taking his broken glasses and tossing them to the ground. He rushed forward again, his feet crushing the shattered glasses even more.

He came at Neo. The rebel ducked under a fast attack and slammed his fist upward into Smith's chest. Smith brought both his fists down onto Neo's shoulders, driving him back.

Smith brought his knee into Neo's stomach and the rebel was thrown backwards into the air. He landed on his back, letting out a breath of air.

Lynx opened fire, Trinity drawing her weapon and doing the same. The Agent twisted through the air, dodging all the bullets. Trinity's gun fell silent, followed quickly by Lynx's. The three guns hit the floor.

Matthews ran forward. Trinity jumped, placing one hand one the ground to propel her out of the way. Matthews stopped and grabbed at her, missing. Lynx leapt, hitting the Agent's back with her foot. He went stumbling forward, turning around and drawing his gun.

As he opened fire, time seemed to slow. Lynx, two feet away, fell backwards to avoid the first bullets. As the gun moved towards Trinity, she kicked at the Agent's hand, sending the gun into the air. It flipped higher and higher, reaching the top part of its flight and beginning to come back down. It had almost reached the ground when a sharp blade slashed through it, severing it into two pieces.

Morpheus stood at the entrance to the subway. He lifted his sword and charged in.

Neo climbed back to his feet, straightening his glasses. Smith waited for him to finish, and then charged in again.

His first attack was a hard punch to the face, shattering Neo's eyewear. The rebel reeled away, bringing his foot up to hit the inside of Smith's knee at the same time. Smith sank backwards, hitting the ground with two hands and continuing his reverse cartwheel to land on his feet.

Neo's glasses hit the ground, creating a small splash. Neo stepped forward again, his hand connecting with Smith's block. Neo leapt into the air, bringing one foot up and into Smith's chin. The program stumbled back, flailing. He gathered himself together and moved forward again.

As their fists connected, they both sensed a disturbance and turned. Two albino Twins stood at the other end of the street.

"Neo," Alpha said. "We've been sent to retrieve you."

Morpheus brought his sword down in a diagonal slash. Matthews jumped back to avoid the attack, and Morpheus reversed the blade, thrusting towards Matthew's stomach.

The Agent hit the blade aside and threw his fist in at Morpheus. The rebel captain took the blow and dropped the blade. Trinity came in from behind, dropping her fist down onto Matthew's neck. The Agent dropped.

"Thanks," Trinity said. "But we lost our chance. The train is gone."

"I have an idea," Lynx said. They listened while she explained it, and Trinity nodded.

"It could work," she said, running towards the street. Lynx took a step forward, but turned back around to grab the sword from the ground. Then she ran to join the woman.

Alpha stepped forward, swinging his blade. Neo ducked away and slammed his foot into the Twin's stomach. Beta leapt into the air, driving both feet into Neo's stomach and sending him stumbling backwards. Beta landed on his feet, flipping his switchblade out.

Smith stepped forward, Alpha swinging his blade at the former Agent. Smith stepped backwards, kicking out to hit the blade away. As the blade came back down, Beta caught it and tossed it at Smith. Smith bent away, and Alpha caught the blade and jammed it into Smith's leg.

As Smith sank to the ground, Neo's foot connected with Alpha's head. Beta slammed his fist into Neo's back and sent him to the ground beside Smith.

"Morpheus."

The captain turned at the sound of a new voice, feminine and strong. He saw a young woman standing close by.

"Who are you?"

"My name is Mukti," she said.

"You're the one who helped Neo. Where is he?"

"The Merovingian has captured him again, but I am here to tell you that your original plan will still work. Trinity will find him, no matter the cost."

Lynx gunned the engine again, sending her motorcycle past the car and even with Trinity's. The woman looked over at Lynx and pointed straight ahead, to a large bridge over a set of train tracks.

Lynx heard a loud sound of screeching metal as the car behind her exploded. She looked back to see a helicopter chasing them, an Agent at the driver's seat. Another Agent manned the guns. He opened fire, and a line of bullets streamed through where Lynx had just been.

Trinity swerved left, dodging another line of fire. She fired blindly over her shoulder, missing the helicopter. She cut across two lanes of traffic towards the off ramp.

Lynx shot forward, weaving in and out of cars. The helicopter fired again, destroying a car in her path. Lynx turned as quickly as possible, making it out of the way. She cut in front of another car, causing it to swerve, spinning wildly, into another car. The Agent lined Lynx up in his sights.

"We can't beat them alone, Mister Anderson," Smith said.

Neo nodded, grabbing Smith's outstretched hand. Smith pulled the rebel to his feet. Alpha flipped his switchblade over, catching it by the sharp edge, and threw it at Smith. Neo smacked the blade away, sending it clattering into the small puddles nearby.

Beta slashed his switchblade at Neo's chest. Smith's foot connected with the blade and sent it spiraling into the air. Neo leapt, higher than any human ever living could, and caught the blade, landing and driving it through Alpha's phased form. The two Twins stepped backwards, regrouping themselves.

Trinity's motorcycle flew over the street. Trinity slid off, falling towards the ground below. The motorcycle slammed into the helicopter. The craft exploded in a ball of fire. Trinity landed on the backseat of Lynx's motorcycle. Lynx hit the gas and sped off towards the bridge.

Alpha and Beta stepped backwards, disappearing into the Chateau. Neo turned to face Smith.

"Until we meet again, Mister Anderson."

Neo walked after the Twins, reappearing inside the room he had just left. Samsara stood there, smiling.

"You're back. Your friends are on the way."

Lynx looked left and saw the train exit the ground and continue its way towards the bridge. She slammed on the pedal and shot forward again, reaching the bridge. She rocketed up the bridge and through the guard rail, hanging in the air before the cycle came crashing down on top of the train. Trinity got off and opened the hatch, dropping into the dining car. Lynx followed suit, slamming the hatch closed behind her and cutting out all light from above.

"Let's go," Trinity's voice came from the darkness.

_We're coming, Neo._


	6. Extraction

**Chapter Five: Extraction**

The door slowly slid open. The Trainman turned, wild hair flying, to stare directly into the cold, hard glasses of freedom fighter Trinity.

"Freeze."

The Trainman froze.

"What do you want?"

"Take us to Neo."

The Trainman threw his head back and laughed.

"No deal. The Merovingian would delete me for sure."

Trinity glared at him. "I'll delete you here and now if you don't."

"I don't think so," he said. "You see, to do that, you'd have to beat me."

Lynx checked left and right before slamming the door open. She hit the back of someone and sent that person flying. He rolled around and stood up, growling.

A Doberman…one of the Merovingian's minions. Lynx raised her sword and charged forward, slashing diagonally. The Doberman fell backwards, growling, and slammed into another door, knocking it open. Lynx looked into the face of three more minions.

"Sorry, wrong car."

They got up and charged.

"Can't we make a deal?" the Trainman asked. "I don't want to hurt you."

Trinity was silent.

"No, huh? Well…"

The Trainman turned slowly, hands raised. He hit a button next to his head, and the train screeched to a stop. Trinity stumbled, and he jumped forward, hitting her gun away. It fell out the window. Trinity steadied herself on the wall and kicked the Trainman in the stomach with both feet. He groaned and fell backwards.

Trinity pressed her attack, dropping back to the floor and kicking out. The Trainman caught her attack and pushed back, forcing Trinity to jump to avoid falling. 

She grabbed onto the ceiling hatch and pulled it open, revealing the blue sky. She hung from the hatch and slammed both feet into the Trainman face, sending him tumbling back into the train lever. It slowly began to move again, building up speed.

Lynx ducked under a slashing claw and stabbed the sword through the first Doberman's belly. She kicked his body off her blade and brought the sword up in time to block another attack, kicking the attacker and sending him sprawling. She raised the sword above her head and brought it spiraling down, slicing through an upraised arm and continuing to sheer off the creature's head.

The third Doberman ran for the edge of the car. Lynx grabbed the dagger from her boot and threw it, hitting the Doberman's back. He hit the ground with a thud two inches from the door.

The Trainman swung the metal bar and hit Trinity in the chest, forcing the air from her body in one quick gasp. She collapsed to her knees, gasping for breath, her vision swimming. She heard two steps and saw his legs fill her vision.

She grabbed hold of his leg and pulled hard, bringing him down level with her. She leapt to her feet in one smooth motion and slammed her foot down, hitting the space where he had been only seconds before. He rose up and grabbed a ladder, disappearing out the top hatch. Trinity pursued.

Fang looked up from his hand of cards. He clearly heard someone pounding on the door. With a growl, he heaved himself from the chair and walked to the door, sliding it open.

Ripper lay on the ground, dead. Fang suddenly knew he had been tricked, and that it was too late. He turned around to see a bright balde descending.

Lynx pulled the blade from the head of the Doberman and slammed the hilt backwards, hitting the face of another. The wounded fighter stumbled backwards, clutching his nose, and Lynx turned, bringing her sword into his neck. He fell.

The other two split up and flanked Lynx. One darted in, slamming a foot into Lynx's hand and making her drop the sword. She leapt into the air and kicked both feet out, hitting them both in the head. Then she dropped, grabbed her sword, and stabbed the first one.

The last Doberman waded in, swinging his heavy arms. Lynx drove the sword home, slaughtering him.

_Almost there…_

As Trinity pulled herself up, the Trainman roared and charged at her. She rolled out of the way, jumping to her feet as he rushed in. He slammed his fist into her shoulder and pushed her sideways. She teetered on the edge for a moment, then pulled herself upright and kicked out. The Trainman caught her blow on his chin and went spinning in the air, landing facedown on another car. Trinity leapt after him.

_One more car…_

Lynx kicked down the door of another car, shoving her blade into the chest of a Doberman. The other fighters scrambled to their feet.

"Let me pass," Lynx warned. "I've already killed many of you today."

"Silly human," one hissed, their leader. He was taller and stronger then the other two. "We cannot die."

And they came forward.

Trinity landed where the Trainman's head had been. He rolled to the side and kicked the inside of her knee, making her fall forward. She rolled and pushed herself to her feet with her arms. The Trainman slammed into her as she regained her balance, and she teetered on the edge of the car.

Lynx slashed out viciously, tracing a line of red blood across the throat of one of the attackers. The leader slammed his shoulder into Lynx's chest, knocking her back into the wall. He took her hand and beat it against the doorframe, causing her to lose her grip on the weapon.

She brought her knee into the leader's stomach and pushed out with both arms, sending him flying into the opposite wall. The Doberman drew a gun, and she kicked him in the stomach, grabbing the gun with her hand and twisting it until it broke loose.

The leader stood back up and sent a glass flying Lynx's way. She fired, shattering the makeshift missile. The Doberman sunk his teeth into her hand. She slammed the Exile's head into the window, shattering glass. He sunk his teeth in harder, and she dropped the gun outside.

The Trainman slammed into Trinity again. She lost her balance and fell towards the ground below. Trinity quickly cleared her mind, and time slowed to a crawl. She saw a gun come flying towards her and grabbed it with one hand. With the other, she reached out and grabbed part of the train flashing past her and landed on a connecter between two cars.

Time returned to normal speed. Trinity pulled herself back onto the roof of the train. The Trainman had already returned to the front car and was climbing looking down. He pulled out his own gun and aimed down, shooting the connecters between the two cars.

"No," Trinity said. She glanced behind her, and a rare smile crept onto her face.

Lynx saw the connecters separate as her car began to lose speed. She knocked the Exile off her and ran for the front car, grabbing a tray on the way out. She jumped as far as she could, catching the edge of the front car and falling. She grimaced as her injured hand hit the metal, but forced the pain away. She landed on the tray and was suddenly being dragged along the tracks.

The leader jumped after her, grabbing onto her feet. She kicked him in the face twice and watched him fall away. Then she pulled herself up into the front car.

Trinity revved the engine and the motorcycle shot along the roof of the train. She saw the Trainman's eyes grow wide with fear as the motorcycle easily leaped the gap. Trinity jumped off, and the motorcycle hit the ceiling and slammed into the Trainman, crushing him.

Trinity landed and climbed back inside. She spotted Lynx, looking tired and sweaty.

"Trouble?" she asked.

"Piece of cake," Lynx said.

The Merovingian tapped his foot impatiently, glancing at his watch.

"Late," he grumbled. As he spoke, he saw the train appear in the distance.

"Excellent."

He turned to Neo. "They'll be here soon, to take you to your new home, where no one will ever be able to find you."

Neo just smiled slightly. The train continued to come in, not slowing slightly. As it got closer, everyone could see that it was missing most of the cars.

"Shit," someone said. "Everyone off the platform!"

Everyone began to scramble. Alpha grabbed Neo roughly and pulled him inside. The door slammed, cutting off Neo's sight. He heard a loud, screeching noise and a huge crashing sound. The door opened again.

The train had slammed headfirst into a wall, stopping. The Merovingian stepped into the tracks, looking inside.

"Trainman?"

A click sounded, and suddenly Trinity was standing there, gun pressed against the head of the Exile leader. He gulped.

"Neo," she said. "Right now. Or we all die."

He nodded slowly, backing away. With a wave, he motioned Alpha forward. Alpha pushed Neo roughly, and he stumbled onto the tracks.

"There," the Merovingian said.

"Trinity," Neo said. "Do you have a plan for getting out of here?"

She nodded, slightly.

"Take us to your hard line," she ordered the Merovingian. He nodded and led the three rebels off through his house to the one hard line nearby. The phone rang, and the Merovingian picked it up and handed it to Lynx.

"Thank you," she said, placing it to her ear. She vanished.

"Um, Trinity…" Neo began. "I don't have a body anymore."

She handed him the phone. "I know."

He placed it to his ear and was yanked from the Matrix, feeling the senses of the real world assault him. He opened his eyes and glanced down at his body.

It was Phoenix's.

Smith took a step, and the five clones stepped out with him. He quickly crossed the street into the large hole left by Mister Anderson's departure.

A Doberman tried to stop him and was quickly assimilated. Soon, Smith found himself in the upper levels of the Chateau. He opened the door to a large bedroom, where the Merovingian slept with a woman that was _not _Persephone.

"Wake up," Smith said. The Merovingian opened his eyes. He tried to scream, but Smith shoved his hand into the Exile's stomach. The new programming spread through him, and the man's struggles stopped.


	7. Down the Rabbit Hole

**

Part Two: Dreaming of Zion

**

_"Zion's more important than you, more important than me, more important than any of us."_****

**

* * *

**

**Chapter One: Down the Rabbit Hole**

The _Nebuchadnezzar _ran low, lights and heat off, creeping towards the main line that would take them to Zion, their home. Ghost kept a wary eye on every screen, looking for Sentinels.

"No signs of movement," he said to Morpheus. "We're clear. But it's a narrow window of opportunity."

"We'll hurry, then," Morpheus said. He spun on his heel, walking towards the cockpit.

Trinity slowly guided the hovercraft over the ruins of the ancient sewer system. As it passed into the main shaft, three figures detached themselves from the roof and slipped after it.

These were the Hunters, the newest creation of the machine army. Modeled after Sentinels, they were colored pitch-black and without lights, making them almost impossible to see by eye alone. Thanks to the latest machine technology, they were just as invisible to the human's primitive radar.

The Hunters were the ultimate stalkers, and the ultimate killers.

"Still no enemies in sight," Neo said.

"Good."

Neo lay back in his seat. "Morpheus, thank you for not abandoning me."

Morpheus smiled, a rare sight. "Neo, do you remember what you did on your first mission into the Matrix? You saved my life. I would never abandon you if there was even the smallest chance that you could return to us. We need you, Neo. Zion needs you."

"Though, I must admit, I don't understand one thing."

'What?"

"How did you manage to put me into Phoenix's body?"

"While you were in the Chateau, Phoenix fought an Exile. He was shot during the battle, while he was exiting the Matrix. Somehow the timing of his wound caused the actual wound to appear here in the real world. We literally pulled a bullet from his chest.

"But he couldn't survive it. He fought against the wound and somehow, using the fact that he had been partly inside the Matrix when wounded, pushed the wound from his body. But the effort tore his brain tissue and killed him…in a sense. Mentally, he was dead, but physically he was not. We managed to hook you into his brain and give you full control of his body."

The lead Hunter dropped right behind the _ Neb, _reaching forward with a long, metal claw and depositing a package on the rear of the hovercraft. The box broadcast the ship's position to the entire machine army.

"Two contacts on the radar!" Myst shouted.

"Where? How?"

"Behind us!"

Morpheus leapt forward and hit the controls. The _Neb _spun wildly, coming to a stop facing the two contacts.

"Hunters…" Myst whispered. 

"Cannons!" Morpheus shouted. "Now! They'll have broadcasted our location! Get ready for a fight, people! Trinity, get us home!"

Trinity slipped into the pilot's seat. Myst felt a swift pain at the thought that Phoenix would normally be the one doing so, and ran back to the Core, yelling for Ghost.

The first Hunter flowed towards the hovercraft, twisting in air. A stream of bullets shot out of it, missing wide.

"Where is it?" Myst said over the radio. "It's too dark!"

Morpheus reached forward and slammed on the _ Neb's _lighting. The Hunters shot out in two directions, splitting up. The first cannon tracked one, firing wildly. The second Hunter wheeled around and shot towards the cockpit, metal arms clicking as it attacked.

A stream of bullets slammed into the front of the machine, which exploded in a ball of flame.

"Nice shot!" Myst yelled. Ghost didn't bother to respond, already turning to face the second machine. The second Hunter darted forward, ducking under a salvo from Ghost's turret and passing out of his range.

"Where is it?" Ghost called.

"I see it!" Myst yelled, opening fire. The Hunter weaved around her shots, stretching forward and connecting with the _Neb. _ He extended two claws and ripped the gun turret open, ducking his head inside. Myst's scream was quickly cut off.

"Shit," said Neo, unbuckling his harness and heading for the rear of the ship. Trinity grimaced, hit the thrusters, and rounded the next turn.

Myst scrambled out of her chair as the Hunter squeezed in through the gun turret. She dashed for the down ladder. The Hunter slammed its arm into her and grabbed her leg, pulling her down and dragging her backward.

She screamed again, kicking at the metal arm. The creature's arm expanded, a long metal spike extending from the limb. He stabbed it down, through her shoulder and into the floor, pinning her. She yelled again, this time in pain.

The hatch swung open and Phoenix's head appeared.

_Neo's head…_

Neo raised his plasma gun above his head and fired, striking the Hunter. It spasmed and collapsed onto the gunner's seat. Neo dropped the gun and pulled himself into the turret, hurrying over to where Myst was pinned.

"Don't," he said as she tried to pull the spike from her shoulder. He grabbed the spike in both hands and stood quickly, yanking it from her shoulder. She gasped in pain.

"Let me," he said, helping her stand and supporting her on one shoulder. She pushed herself off him and stumbled, hitting a wall.

"What?" Neo asked, coming to her side. "Did I hurt you?"

"No…" Myst mumbled. "It's just…"

"What?"

"It's strange, alright? Phoenix and I were lovers once, before he left the _Logos. _We were just reconnecting…and he died. And you're in his body…it's a strange feeling. I'm confused. Physically, he's there, but mentally it's you. I'm just not sure what to do anymore."

Myst gave a choked little laugh and turned away.

"It's fine, I'll be okay."

Neo grabbed her shoulder and turned her back around.

"It's not "fine." You have a good point. I've never had to go through anything like this in my life, and for that I'm eternally grateful. But I've lost loved ones. Sometimes, after you lose someone, you think you see them everywhere. And that's all Phoenix is right now. Just a figment of your imagination. But I'm still here Myst, and I can't do for you what he did, but I _can _protect you. And I will."

Morpheus leaned forward and hit the radio. "Neo? What's happening?"

Neo's answer came back, and Morpheus thought he could hear faint crying in the background. "We're fine here, sir. Just talking."

Morpheus nodded and called Ghost. "Ghost?"

"Yes?"

"At one point during the fight, I thought I had seen a third figure on the radar. Did you see anything like that?"

"Actually, I did. I thought it had just been me…"

"Do you know where it went?"

"No…"

Then it was there. The third Hunter swung down from its space on top of the _Neb _and slammed through the forward view port. Trinity ducked left, hitting the controls and sending the _Neb _into a wild spin. The Hunter raised its arms to attack. Morpheus ducked under the attacking machine and out onto the floor.

"Trinity!" he shouted.

"Fine!" she grunted, kicking the Hunter twice in the face. It turned its attention to the woman, clicking its claws in an almost hungering way. Morpheus grabbed the cable leading from the radar to the Core and yanked it off the wall.

The hiss of sparks attracted the Hunter's attention again. It turned to Morpheus, slamming him into the bulkhead with its powerful arms. Trinity jumped up and wrapped her arms around the machine, wrestling with it. Morpheus pushed forward with the cable, driving it home into the Hunter's face. It sparked and fell dead.

"Trinity?"

'Yes?"

"We need to go. Now. The Sentinels are coming, and we have no radar."

"Already on it, sir."

Later that night, as the generators hummed around them, Neo and Trinity met in the Core.

"I've missed you," he said, kissing her. She kissed back, but seemed cold and distant. He could sense it. Pulling away, he asked what was wrong.

"It's a little strange," Trinity admitted. "Mentally, you're there, but physically…you're not. I'm not sure exactly how it works."

"I'm still the same," Neo said.

"I'm not so sure."

"Let's see if I can change your mind."

They had powered down the _Neb _and set it on the cavern floor. Ghost crouched on the top, scanning the surrounding tunnels. He spotted a faint light in the distance and called it in.

"Thanks, Ghost. Stand by for more instructions."

Morpheus clicked off the radio. A new transmission cut across the comm waves.

_"Hello can anyone here us? This is the _ Blackened Sky. _Can anyone hear us? We are under pursuit by Sentinels. Can anyone help us?"_

Morpheus hit the radio again. "Ghost, get inside and man the turret."

Trinity and Neo rushed into the cockpit.

"We have reports of a ship being pursued by Sentinels," Morpheus said. "We're going in."

Trinity took the controls, while Neo hung back and closed his eyes.

"What's the ship's name?"

"_Blackened Sky._"

"Never heard of it."

"Neither had I."

Neo sat down and began accessing the rebel's battlenet. 

"Stop!" he yelled. "There is no _Blackened Sky!"_

Trinity jammed the _Neb _right, and they slid into another cavern. Sentinels leapt form holes in the wall, converging on the _Neb._

"EMP!" Neo yelled.

"We can't," Morpheus said. "Punch it, Trinity."

The _Neb _shot ahead of the Sentinel horde.

Two Sentinels jumped ahead of the rest, firing waves of blue energy towards the _Neb. _Trinity skillfully avoided each blow, while Ghost turned one Sentinel, then the other, into dust.

"What was that?"

"I don't know," Morpheus said. "But if the machines have decided to use some form of concentrated EMPs, we could be in serious trouble."

"Turn," Trinity announced. They both grabbed hold as Trinity veered sharply around and into the main pipe.

"Call Zion," she said. "We're coming in."

Three more Sentinels spread out, firing the blue waves of energy. Ghost turned his fire on one, quickly shattering it. The second dived under his range and began to fire again, scoring a hit on the _Neb's _ underside.

Nothing happened.

Neo frowned. Something felt wrong. He reached forward and began to change the channel of the radio until he came across a loud buzzing and hissing sound.

"Normal Sentinel chatter," Morpheus said.

"Can you drown it out?"

"Sure."

The noise faded away, and Neo heard a pulsing burst of sound every few seconds. He turned towards the view port and watched the Sentinel fire.

"They're not attacking," he said. "They're communicating."

Ghost destroyed the third Sentinel with a quick burst from his cannon. Five more leapt forward, firing as they came.

Neo stared at the code that shot across his screen every time the Sentinels fired.

"I'm not sure…" he said. "It's some sort of reactivation code."

One Sentinel slipped past Ghost's fire to the ruined turret where the Hunter still lay and fired. The blue energy struck the downed machine. Its systems slowly came online. The red eye glowed brightly.

Neo ran towards the gun turret where the Hunter still lay, scooping a plasma gun from the floor as he ran. He kicked the hatch open and climbed up, spotting the Hunter as it powered up.

It stared at him and fired its cutting beam straight through his chest.

Trinity suddenly lost control of the ship. The _ Neb _began to spin. Trinity fought to steady it, but to no avail. The hovercraft's rear end swung about and slammed into a rock, tearing off. The wreckage came to a rest on the cold ground.

Trinity ran to the Core as fast as her legs would carry her.

"No!" Trinity cried, seeing Neo's body lying on the ground with a hole through it. She sunk to her knees. Morpheus appeared in the doorway, holding a plasma gun. He fired. The Hunter ducked under the blast, shooting towards Morpheus and knocking him over. The machine flew around the room, ripping out cables and wires from the central unit.

The Hunter reared up before Trinity, clicking both killing claws. She squeezed Neo's hand.

"Guess this is where it ends," she muttered.

The Hunter suddenly seized up, blue sparks flying out of it. It hung there for a second and then fell to the floor. 

"What?" Trinity mumbled.

Neo opened his eyes.

"Neo!"

Neo looked down at his chest and shrugged. "It's not my body…"

Trinity laughed and leaned down to kiss him.

Myst came running in. She glanced at Phoenix – _ NEO _– and Trinity and shoved away the quick burst of pain.

"What happened?" she asked. "The Sentinels outside all just collapsed."

Neo smiled.

"We need to get to Zion," Morpheus said. "Any suggestions?"

Lynx pointed at the map. "Here."

Morpheus looked where she pointed. "Yes…"

"There's an access shaft," she said. "We cans slide down that straight into Zion. It's too small for a Sentinel, but we'll be able to fit through with ease."

"Let's go," Morpheus said.

A long line of humans left the _Neb, _ running towards the access shaft across the cavern. A single Hunter detached from the ceiling and broadcast a short radio message to the central control room.

_target inside Zion_

The reply came back quickly.

_ATTACK_

The Hunter relayed the commands to the Sentinels surrounding Zion and started off to join the fight.

Neo flipped open the hatch and motioned for Trinity to jump in. She disappeared down the hole, followed quickly by Myst and Ghost. Morpheus followed suit, and Neo took one last sweep of the area before jumping down himself.

As he slid down the pipe, he noticed a faint glow at the end of the tunnel. It was yellow – the color of the sun that would never shine.

And the color of fire.


End file.
